Add recipes for Python ctypes interface (#16)

docs/_archives/recipes/interfaces/pyapi/dftb_in.hsd

@@ -0,0 +1,52 @@
+Geometry = GenFormat {
+
+    6  S
+ Ti  O
+    1 1    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    2 1    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    3 2    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    4 2    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    5 2    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    6 2    0.0000000000E+00  0.0000000000E+00  0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    1.0000000000E+02    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    1.0000000000E+02    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    1.0000000000E+02
+
+}
+
+Driver = {}
+
+Hamiltonian = DFTB {
+
+  Scc = Yes
+  MaxSccIterations = 100
+  SccTolerance = 1.00e-05
+
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+
+  MaxAngularMomentum {
+    Ti = "d"
+    O  = "p"
+  }
+
+  KPointsAndWeights = SupercellFolding {
+    4   0   0
+    0   4   0
+    0   0   4
+    0.5 0.5 0.5
+  }
+
+}
+
+Analysis {
+  CalculateForces = Yes
+}
+
+ParserOptions {
+  ParserVersion = 8
+}

docs/_archives/recipes/interfaces/pyapi/extpot/dftb_in.hsd

@@ -0,0 +1,36 @@
+Geometry = GenFormat {
+ 3  C
+  O H
+     1    1    0.00000000000E+00   0.00000000000E+00   0.00000000000E+00
+     2    2    0.00000000000E+00   0.00000000000E+00   0.00000000000E+00
+     3    2    0.00000000000E+00   0.00000000000E+00   0.00000000000E+00
+}
+
+Driver = {}
+
+Hamiltonian = DFTB {
+
+  SCC = Yes
+  SCCTolerance = 1.00E-012
+  MaxSCCIterations = 1000
+
+  MaxAngularMomentum = {
+    O = "p"
+    H = "s"
+  }
+
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix  = ".skf"
+  }
+
+}
+
+Analysis = {
+  CalculateForces = Yes
+}
+
+ParserOptions = {
+  ParserVersion = 8
+}

docs/_archives/recipes/interfaces/pyapi/extpot/pyapiExtpot.py

@@ -0,0 +1,69 @@
+import numpy as np
+import dftbplus
+
+
+LIB_PATH = '/home/user/libdftbplus'
+
+
+def main():
+    '''Main driver routine.'''
+
+    # coordinates of H2O, in atomic units
+    coords = np.array([
+        [0.000000000000000E+00, -0.188972598857892E+01,  0.000000000000000E+00],
+        [0.000000000000000E+00,  0.000000000000000E+00,  0.147977639152057E+01],
+        [0.000000000000000E+00,  0.000000000000000E+00, -0.147977639152057E+01]])
+
+    # the values of extpot and extpotgrad used here were
+    # taken from file: test/api/mm/testers/test_extpot.f90
+    extpot = np.array([-0.025850198503435,
+                       -0.005996294763958,
+                       -0.022919371690684])
+
+    extpotgrad = np.array([
+        [0.035702717378527,  0.011677956375860, 0.009766745155626],
+        [0.023243271928971, -0.000046945156575, 0.004850533043745],
+        [0.016384005706180,  0.004608295375551, 0.005401080774962]])
+
+    cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
+                              hsdpath='dftb_in.hsd',
+                              logfile='log.log')
+
+    # set geometry
+    cdftb.set_geometry(coords, latvecs=None)
+
+    # set external potential and its gradients
+    cdftb.set_external_potential(extpot, extpotgrad=extpotgrad)
+
+    # get number of atoms
+    natoms = cdftb.get_nr_atoms()
+
+    # calculate energy, forces and Gross charges
+    merminen = cdftb.get_energy()
+    gradients = cdftb.get_gradients()
+    grosschgs = cdftb.get_gross_charges()
+
+    # finalize DFTB+ and clean up
+    cdftb.close()
+
+    # print obtained nr. of atoms
+    print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
+
+    # print obtained mermin free energy
+    print('(H2O) Obtained Mermin-energy: {:15.10f}'.format(merminen))
+
+    # print obtained gradients
+    print('(H2O) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
+          .format(*gradients[0]))
+    print('(H2O) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'
+          .format(*gradients[1]))
+    print('(H2O) Obtained gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}'
+          .format(*gradients[2]))
+
+    # print obtained Gross charges
+    print('(H2O) Obtained Gross charges: {:15.10f} {:15.10f}'
+          .format(*grosschgs))
+
+
+if __name__ == "__main__":
+    main()

docs/_archives/recipes/interfaces/pyapi/extpot/run.sh

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+#!/bin/bash
+set -e
+python3 ./pyapiExtpot.py > output
+

docs/_archives/recipes/interfaces/pyapi/pyapi.py

@@ -0,0 +1,67 @@
+import numpy as np
+import dftbplus
+
+
+LIB_PATH = '/home/user/libdftbplus'
+
+# DFTB+ conversion factors
+# (according to prog/dftb+/lib_common/constants.F90)
+BOHR__AA = 0.529177249
+AA__BOHR = 1 / BOHR__AA
+
+
+def main():
+    '''Main driver routine.'''
+
+    # coordinates of TiO2, in atomic units
+    coords = np.array([
+        [-0.016726922839251,  0.016725329441158, -0.000003204152532],
+        [-0.016726505918979,  1.920201169305565, -7.297102897292027],
+        [ 0.017412997824265, -0.024318617967798,  2.005339137853385],
+        [ 1.920770753428742, -0.024319922392223, -4.437737763954652],
+        [ 0.024319174400169, -0.017404302527510, -2.005347277168561],
+        [ 0.024317270342179,  1.886164739806594, -5.291732430733527]])
+    coords *= AA__BOHR
+
+    # lattice vectors of TiO2, in atomic units
+    latvecs = np.array([
+        [-1.903471721000000,  1.903471721000000,  4.864738245000000],
+        [ 1.903471721000000, -1.903471721000000,  4.864738245000000],
+        [ 1.903471721000000,  1.903471721000000, -4.864738245000000]])
+    latvecs *= AA__BOHR
+
+    cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
+                              hsdpath='dftb_in.hsd',
+                              logfile='TiO2.log')
+
+    # set geometry
+    cdftb.set_geometry(coords, latvecs=latvecs)
+
+    # get number of atoms
+    natoms = cdftb.get_nr_atoms()
+
+    # calculate energy, gradients and Gross charges
+    merminen = cdftb.get_energy()
+    gradients = cdftb.get_gradients()
+    grosschgs = cdftb.get_gross_charges()
+
+    # finalize DFTB+ and clean up
+    cdftb.close()
+
+    # print obtained nr. of atoms
+    print('(TiO2) Obtained nr. of atoms: {:d}'.format(natoms))
+
+    # print obtained mermin free energy
+    print('(TiO2) Obtained Mermin-energy: {:15.10f}'.format(merminen))
+
+    # print obtained gradients
+    print('(TiO2) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
+          .format(*gradients[0]))
+
+    # print obtained Gross charges
+    print('''(TiO2) Obtained Gross charges: {:15.10f} {:15.10f}
+          {:15.10f} {:15.10f} {:15.10f} {:15.10f}'''.format(*grosschgs))
+
+
+if __name__ == "__main__":
+    main()

docs/_archives/recipes/interfaces/pyapi/qdepextpot/dftb_in.hsd

@@ -0,0 +1,55 @@
+Geometry = GenFormat {
+ 3  C
+  O H
+     1    1    0.00000000000E+00  -0.10000000000E+01   0.00000000000E+00
+     2    2    0.00000000000E+00   0.00000000000E+00   0.78306400000E+00
+     3    2    0.00000000000E+00   0.00000000000E+00  -0.78306400000E+00
+}
+
+Driver {}
+
+Hamiltonian = DFTB {
+
+  SCC = Yes
+  SCCTolerance = 1.00E-10
+  MaxSCCIterations = 1000
+
+  Mixer = Broyden {}
+
+  MaxAngularMomentum {
+    O = "p"
+    H = "s"
+  }
+
+  Filling = Fermi {
+    Temperature [Kelvin] = 1.0E-8
+  }
+
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix  = ".skf"
+  }
+
+#  ElectricField {
+#
+#    PointCharges {
+#
+#      CoordsAndCharges {
+#        -0.944863438887178  -9.44863438887178  1.70075418999692    2.5
+#         4.34637181888102   -5.85815332110050  2.64561762888410   -1.9
+#      }
+#
+#    }
+#
+#  }
+
+}
+
+Analysis {
+  CalculateForces = Yes
+}
+
+ParserOptions {
+  ParserVersion = 6
+}